NP-MRD: Showing NP-Card for epirubicin (NP0253363)

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Record Information

Version

2.0

Created at

2022-09-07 17:13:01 UTC

Updated at

2022-09-07 17:13:01 UTC

NP-MRD ID

NP0253363

Secondary Accession Numbers

None

Natural Product Identification

Common Name

epirubicin

Description

Epirubicin, also known as 4'-epiadriamycin or farmorubicin, belongs to the class of organic compounds known as anthracyclines. These are polyketides containing a tetracenequinone ring structure with a sugar attached by glycosidic linkage. Epirubicin is a drug which is used for use as a component of adjuvant therapy in patients with evidence of axillary node tumor involvement following resection of primary breast cancer. Epirubicin is a very strong basic compound (based on its pKa). Epirubicin is a potentially toxic compound. epirubicin is found in Streptomyces venezuelae. epirubicin was first documented in 2001 (PMID: 11432615). An anthracycline that is the 4'-epi-isomer of doxorubicin (PMID: 15821120) (PMID: 16005104) (PMID: 17604344) (PMID: 18838875).

Structure

MOL 3D MOL SDF PDB SMILES InChI

445
  Mrv0541 02231214412D          

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M  END

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445
  Mrv0541 02231214412D          

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 17 18  2  0  0  0  0
 17 24  1  0  0  0  0
 18 26  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 29  1  1  0  0  0
 24 27  2  0  0  0  0
 25 30  1  0  0  0  0
 26 28  2  0  0  0  0
 27 28  1  0  0  0  0
 27 31  1  0  0  0  0
 28 32  1  0  0  0  0
 31 33  1  0  0  0  0
 32 34  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 34 36  1  0  0  0  0
 35 37  2  0  0  0  0
 36 38  2  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0253363

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=CC2=C1C(=O)C1=C(O)C3=C(C[C@](O)(C[C@@H]3O[C@H]3C[C@H](N)[C@@H](O)[C@H](C)O3)C(=O)CO)C(O)=C1C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H29NO11/c1-10-22(31)13(28)6-17(38-10)39-15-8-27(36,16(30)9-29)7-12-19(15)26(35)21-20(24(12)33)23(32)11-4-3-5-14(37-2)18(11)25(21)34/h3-5,10,13,15,17,22,29,31,33,35-36H,6-9,28H2,1-2H3/t10-,13-,15-,17-,22-,27-/m0/s1

> <INCHI_KEY>
AOJJSUZBOXZQNB-VTZDEGQISA-N

> <FORMULA>
C27H29NO11

> <MOLECULAR_WEIGHT>
543.5193

> <EXACT_MASS>
543.174060775

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
53.88131441703695

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(8S,10S)-10-{[(2R,4S,5R,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-6,8,11-trihydroxy-8-(2-hydroxyacetyl)-1-methoxy-5,7,8,9,10,12-hexahydrotetracene-5,12-dione

> <ALOGPS_LOGP>
1.41

> <JCHEM_LOGP>
0.9164216415385819

> <ALOGPS_LOGS>
-2.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.02035317339782

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.530879900606058

> <JCHEM_PKA_STRONGEST_BASIC>
8.935690197370455

> <JCHEM_POLAR_SURFACE_AREA>
206.07

> <JCHEM_REFRACTIVITY>
134.59369999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.18e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
epirubicin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 445                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       9.211   0.777   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       6.544   0.807   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       7.033  -4.495   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.912   3.918   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      11.904   0.723   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      11.904  -5.437   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.483  -1.834   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.953  -4.507   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      14.596   0.777   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      14.596  -5.490   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.426   0.843   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       6.597   5.427   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       9.193  -0.763   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.798  -3.159   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.798  -1.555   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.193  -3.950   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.570  -1.587   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.570  -3.127   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.886   1.562   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.904   3.102   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.579   3.887   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.237   3.133   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.219   1.593   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.904  -0.817   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.258  -3.165   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      11.904  -3.897   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.237  -1.587   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      13.237  -3.127   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.877   0.838   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.493  -4.501   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      14.614  -0.763   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      14.614  -3.950   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      16.009  -1.555   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      16.009  -3.159   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      17.443  -0.697   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      17.443  -4.016   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      18.897  -1.521   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      18.897  -3.192   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      18.750   1.628   0.000  0.00  0.00           C+0
CONECT    1   13   19                                                       
CONECT    2   19   23                                                       
CONECT    3   14                                                            
CONECT    4   22                                                            
CONECT    5   24                                                            
CONECT    6   26                                                            
CONECT    7   25                                                            
CONECT    8   30                                                            
CONECT    9   31                                                            
CONECT   10   32                                                            
CONECT   11   35   39                                                       
CONECT   12   21                                                            
CONECT   13    1   15   17                                                  
CONECT   14    3   15   16   25                                             
CONECT   15   13   14                                                       
CONECT   16   14   18                                                       
CONECT   17   13   18   24                                                  
CONECT   18   16   17   26                                                  
CONECT   19    1    2   20                                                  
CONECT   20   19   21                                                       
CONECT   21   12   20   22                                                  
CONECT   22    4   21   23                                                  
CONECT   23    2   22   29                                                  
CONECT   24    5   17   27                                                  
CONECT   25    7   14   30                                                  
CONECT   26    6   18   28                                                  
CONECT   27   24   28   31                                                  
CONECT   28   26   27   32                                                  
CONECT   29   23                                                            
CONECT   30    8   25                                                       
CONECT   31    9   27   33                                                  
CONECT   32   10   28   34                                                  
CONECT   33   31   34   35                                                  
CONECT   34   32   33   36                                                  
CONECT   35   11   33   37                                                  
CONECT   36   34   38                                                       
CONECT   37   35   38                                                       
CONECT   38   36   37                                                       
CONECT   39   11                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Value	Source
4'-Epiadriamycin	ChEBI
Epiadriamycin	ChEBI
Epirubicina	ChEBI
Epirubicine	ChEBI
Epirubicinum	ChEBI
Pidorubicina	ChEBI
Pidorubicine	ChEBI
Pidorubicinum	ChEBI
Farmorubicin	Kegg
Ellence	HMDB
Farmorubicine	HMDB
IMI 28	HMDB
IMI28	HMDB
Lemery brand OF epirubicin hydrochloride	HMDB
Pharmorubicin	HMDB
Cell pharm brand OF epirubicin	HMDB
4' Epi adriamycin	HMDB
4' Epi DXR	HMDB
4' Epiadriamycin	HMDB
4' Epidoxorubicin	HMDB
4'-Epi-adriamycin	HMDB
4'-Epi-doxorubicin	HMDB
EPIcell	HMDB
Farmorubicina	HMDB
4'-Epidoxorubicin	HMDB
EPI cell	HMDB
Hydrochloride, epirubicin	HMDB
IMI-28	HMDB
4' Epi doxorubicin	HMDB
4'-Epi-DXR	HMDB
EPI-cell	HMDB
Epilem	HMDB
Epirubicin hydrochloride	HMDB
Kenfarma brand OF epirubicin hydrochloride	HMDB
Pfizer brand OF epirubicin hydrochloride	HMDB
Epirubicin	ChEBI

Chemical Formula

C₂₇H₂₉NO₁₁

Average Mass

543.5193 Da

Monoisotopic Mass

543.17406 Da

IUPAC Name

(8S,10S)-10-{[(2R,4S,5R,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-6,8,11-trihydroxy-8-(2-hydroxyacetyl)-1-methoxy-5,7,8,9,10,12-hexahydrotetracene-5,12-dione

Traditional Name

epirubicin

CAS Registry Number

Not Available

SMILES

COC1=CC=CC2=C1C(=O)C1=C(O)C3=C(C[C@](O)(C[C@@H]3O[C@H]3C[C@H](N)[C@@H](O)[C@H](C)O3)C(=O)CO)C(O)=C1C2=O

InChI Identifier

InChI=1S/C27H29NO11/c1-10-22(31)13(28)6-17(38-10)39-15-8-27(36,16(30)9-29)7-12-19(15)26(35)21-20(24(12)33)23(32)11-4-3-5-14(37-2)18(11)25(21)34/h3-5,10,13,15,17,22,29,31,33,35-36H,6-9,28H2,1-2H3/t10-,13-,15-,17-,22-,27-/m0/s1

InChI Key

AOJJSUZBOXZQNB-VTZDEGQISA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces venezuelae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthracyclines. These are polyketides containing a tetracenequinone ring structure with a sugar attached by glycosidic linkage.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Anthracyclines

Sub Class

Not Available

Direct Parent

Anthracyclines

Alternative Parents

Substituents

Anthracycline
Anthracyclinone-skeleton
Aminoglycoside core
Tetracenequinone
9,10-anthraquinone
1,4-anthraquinone
Anthracene
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Tetralin
Aryl ketone
Anisole
Amino saccharide
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Vinylogous acid
Tertiary alcohol
Alpha-hydroxy ketone
Secondary alcohol
1,2-aminoalcohol
Ketone
Acetal
Organoheterocyclic compound
Polyol
Ether
Oxacycle
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organic nitrogen compound
Amine
Primary amine
Primary alcohol
Primary aliphatic amine
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

quinone (CHEBI:47898 )
monosaccharide derivative (CHEBI:47898 )
anthracycline antibiotic (CHEBI:47898 )
aminoglycoside (CHEBI:47898 )
deoxy hexoside (CHEBI:47898 )
anthracycline (CHEBI:47898 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	1.41	ALOGPS
logP	0.92	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	9.53	ChemAxon
pKa (Strongest Basic)	8.94	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	206.07 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	134.59 m³·mol⁻¹	ChemAxon
Polarizability	53.88 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0014588

DrugBank ID

DB00445

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

38201

KEGG Compound ID

C11230

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Epirubicin

METLIN ID

Not Available

PubChem Compound

41867

PDB ID

Not Available

ChEBI ID

47898

Good Scents ID

Not Available

References

General References

Razis ED, Fountzilas G: Paclitaxel: epirubicin in metastatic breast cancer--a review. Ann Oncol. 2001 May;12(5):593-8. doi: 10.1023/a:1011108807105. [PubMed:11432615 ]
Feher O, Vodvarka P, Jassem J, Morack G, Advani SH, Khoo KS, Doval DC, Ermisch S, Roychowdhury D, Miller MA, von Minckwitz G: First-line gemcitabine versus epirubicin in postmenopausal women aged 60 or older with metastatic breast cancer: a multicenter, randomized, phase III study. Ann Oncol. 2005 Jun;16(6):899-908. doi: 10.1093/annonc/mdi181. Epub 2005 Apr 8. [PubMed:15821120 ]
Berghmans T, Lafitte JJ, Paesmans M, Stach B, Berchier MC, Wackenier P, Lecomte J, Collon T, Mommen P, Sculier JP: A phase II study evaluating the cisplatin and epirubicin combination in patients with unresectable malignant pleural mesothelioma. Lung Cancer. 2005 Oct;50(1):75-82. doi: 10.1016/j.lungcan.2005.05.007. [PubMed:16005104 ]
Iwakiri T, Okumura M, Hidaka M, Kumagai Y, Ichihara E, Kawano Y, Arimori K: Inhibition of carrier-mediated uptake of epirubicin reduces cytotoxicity in primary culture of rat hepatocytes. J Appl Toxicol. 2008 Apr;28(3):329-36. doi: 10.1002/jat.1283. [PubMed:17604344 ]
Goff LW, Rothenberg ML, Lockhart AC, Roth BJ, VerMeulen WL, Chan E, Berlin JD: A phase I trial of irinotecan alternating with epirubicin in patients with advanced malignancies. Am J Clin Oncol. 2008 Oct;31(5):413-6. doi: 10.1097/COC.0b013e318168ef2a. [PubMed:18838875 ]
LOTUS database [Link]

Showing NP-Card for epirubicin (NP0253363)

MOL for NP0253363 (epirubicin)

3D MOL for NP0253363 (epirubicin)

3D SDF for NP0253363 (epirubicin)

3D-SDF for NP0253363 (epirubicin)

PDB for NP0253363 (epirubicin)

3D PDB for NP0253363 (epirubicin)

SMILES for NP0253363 (epirubicin)

INCHI for NP0253363 (epirubicin)

Structure for NP0253363 (epirubicin)

3D Structure for NP0253363 (epirubicin)